scholarly journals Comparison of the Abundance and Community Structure of N-Cycling Bacteria in Paddy Rhizosphere Soil under Different Rice Cultivation Patterns

2018 ◽  
Vol 19 (12) ◽  
pp. 3772 ◽  
Author(s):  
Xiaomei Yi ◽  
Jing Yuan ◽  
Yuanhong Zhu ◽  
Xiaojian Yi ◽  
Qi Zhao ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Rhizosphere Soil ◽  
N Cycling ◽  
Rice Cultivation ◽  
Total Carbon ◽  
Nitrifying Bacteria ◽  
Gene Copy ◽  
Nirs Gene

Eco-agricultural systems aim to reduce the use of chemical fertilizers in order to improve sustainable production and maintain a healthy ecosystem. The aim of this study was to explore the effects of rice-frog farming on the bacterial community and N-cycling microbes in paddy rhizosphere soil. This experiment involved three rice cultivation patterns: Conventionally cultivated rice (CR), green rice-frog farming (GR), and organic rice-frog farming (OR). The rice yield, paddy soil enzyme activities, physicochemical variables and bacterial and N-cycling bacterial abundances were quantitatively analyzed. Rice-frog cultivations significantly increased soil protease, nitrate and reductase activity. Additionally, the nirS gene copy number and the relative abundance of denitrifying bacteria also increased, however urease activity and the relative abundance of nitrifying bacteria significantly decreased. The bacterial community richness and diversity of OR soil was significantly higher than that of the GR or CR soil. Nitrogen use efficiency (NUE) of GR was highest. The N-cycling bacterial community was positively correlated with the total carbon (TC), total nitrogren (TN) and carbon to nitrogen (C:N) ratio. The present work strengthens our current understanding of the soil bacterial community structure and its functions under rice-frog farming. The present work also provides certain theoretical support for the selection of rational rice cultivation patterns.

scholarly journals The impacts of a biochar application on selected soil properties and bacterial communities in an Albic Clayic Luvisol

2020 ◽  
Vol 15 (No. 2) ◽  
pp. 85-92
Author(s):  
Chengsen Zhao ◽  
Qingqing Xu ◽  
Lin Chen ◽  
Xiaoqing Li ◽  
Yutian Meng ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Soil Properties ◽  
Bulk Density ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Soil Layer ◽  
Total Carbon ◽  
Soil Bacterial

In this four-year study, we focused on the impacts of a biochar application on physicochemical soil properties (soil total carbon, total nitrogen, total potassium, total phosphorus, available nitrogen, available potassium, available phosphorus, pH, bulk density and moisture) and bacterial communities in an Albic Clayic Luvisol. The biochar was applied to plots only once with rates of 0, 10, 20 and 30 t/ha at the beginning of the experiment. The soil samples were collected from the surface (0–10 cm) and second depth (10–20 cm) soil layers after four years. The results showed that that the soil total carbon (TC) and pH increased, but the soil bulk density (BD) decreased with the biochar application. The soil bacterial sequences determined by the Illumina MiSeq method resulted in a decrease in the relative abundance of Acidobacteria, but an increase in the Actinobacteria with the biochar application. The bacterial diversity was significantly influenced by the biochar application. The nonmetric multidimensional scaling (NMDS) and canonical correspondence analysis (CCA) indicated that the soil bacterial community structure was affected by both the biochar addition and the soil depth. The Mantel test analysis indicated that the bacterial community structure significantly correlated to a soil with a pH (r = 0.525, P = 0.001), bulk density (r = 0.539, P = 0.001) and TC (r = 0.519, P = 0.002) only. In addition, most of the differences in the soil properties, bacterial relative abundance and community composition in the second depth soil layer were greater than those in the surface soil layer.

scholarly journals Effects of Different Tillage Methods on Bacterial Community and Enzyme Activity of Rhizosphere of Flue-Cured Tobacco in Yunnan Mountains

2021 ◽  
Vol 25 (02) ◽  
pp. 345-353
Author(s):  
Wenjie Tong
Keyword(s):  
Enzyme Activity ◽  
Community Structure ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Ecological Niche ◽  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Shannon Index ◽  
Tillage Methods

The microbial activity and soil enzyme activity are closely related to soil ecological functions. In this study, a flue-cured tobacco (Nicotiana tabacum) variety, K326, was planted and subjected to tillage methods of 20 cm of rotary tillage (control, RT20), 30 cm of deep tillage (DT30), 30 cm (ST30) and 40 cm (ST40) of subsoiling tillage. The expression profiling was conducted using Illumina MiSeq high-throughput sequencing, and the changes of bacterial community structure and enzyme activity in the rhizosphere soil under different tillage treatments were assessed. In the results, the DT30, ST30 and ST40 measures significantly reduced activity of catalase, increased the activities of urease, acid phosphatase and cellulose, and increased the diversity and richness of bacterial communities in the rhizosphere soil. Compared to RT20 (control), the Shannon index of DT30 treatment increased by 3.58%, the Simpson index decreased by 47.46% and the ACE and Chao1 indexes of ST40 treatment increased by 2.77 and 3.38%, respectively. At the phylum and genus levels, the dominant bacterial communities and relative abundance of the bacterial communities under different tillage treatments were significantly different. Compared with RT20, the DT30, ST30 and ST40 treatments increased the relative abundance of Gemmatimonadetes phylum by 30.93, 20.97 and 11.44% and the relative abundance of Nitrospirae phylum increased by 54.55, 22.73 and 11.36%, respectively. In addition, the relative abundances of beneficial microorganisms such as Nocardioides, Gemmatimonas, and Sphingomonas genus in DT30 and ST30, ST40 treatments were more than control (RT20) treatments. In conclusion, the different ecological niche may create by great disturbance to soil in DT and ST treatments, the selection and adaptation of different microorganisms to the ecological niche may result in great changes in microbial species composition and community structure. © 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers © 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers©

Characterization of Bacterial Community Structure in Rhizosphere Soil of Grain Legumes

2005 ◽  
Vol 49 (3) ◽  
pp. 407-415 ◽  
Author(s):  
S. Sharma ◽  
M.K. Aneja ◽  
J. Mayer ◽  
J.C. Munch ◽  
M. Schloter
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Rhizosphere Soil ◽  
Grain Legumes

scholarly journals Effects of biochar on waterlogging and the associated change in micro-ecological environment of maize rhizosphere soil in saline-alkali land

BioResources ◽  
2020 ◽  
Vol 15 (4) ◽  
pp. 9303-9323
Author(s):  
Zhihui Wang ◽  
Dawei Yin ◽  
Hongyi Wang ◽  
Changjiang Zhao ◽  
Zuotong Li
Keyword(s):  
Bacterial Community ◽  
Soil Respiration ◽  
Bulk Density ◽  
Relative Abundance ◽  
Rhizosphere Soil ◽  
Chemical Properties ◽  
Northern China ◽  
Available Phosphorus ◽  
Available Nitrogen ◽  
Maize Rhizosphere

Saline-alkali soils of northern China are prone to waterlogging after degradation caused by overuse. The effects of biochar (40 t/ha) were tested relative to the physico-chemical properties of maize rhizosphere soil, the composition and function of the soil bacterial community, and its response to sudden waterlogging. Biochar treatment decreased the pH and bulk density of the soil and increased soil organic carbon (SOC), available nitrogen (AN), and available phosphorus (AP). The relative abundance of bacteria (Proteobacteria, Actinobacteria, Bacteroidetes, and Nitrospirae) also increased, along with the activities of soil enzymes, such as dehydrogenase, β-glucosidase, and alkaline phosphomonoester. The response of soil microbial enzymes to biochar addition was induced by changes in the soil physical properties (pH, soil moisture content, and soil respiration (BR)). Changes in the bacterial community structure were driven by soil nutrients and physical characteristics (AN, AP, SOC, pH, moisture, water-stable aggregate stability rate, BR, and bulk density). After waterlogging, soil with biochar demonstrated high water permeability and improved soil respiration. The relative abundance of soil bacteria and enzyme activities remained higher in the biochar plot than in the no-biochar plot. Biochar maintained the growth and vitality of maize roots in unfavorable environmental conditions, thus ensuring high yields.

scholarly journals Difference in Rhizosphere Soil Bacterial Community was among Six Cinnamomum camphora Chemotypes

2021 ◽  
Author(s):  
Zufei Xiao ◽  
Beihong Zhang ◽  
Yangbao Wang ◽  
Zhinong Jin ◽  
Feng Li ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Rhizosphere Soil ◽  
Soil Nutrient ◽  
Soil Bacterial Community ◽  
Cinnamomum Camphora ◽  
Close Relationship ◽  
Soil Bacterial

Abstract: Plant types and soil bacterial communities had a close relationship, understanding the profound association between them contributes to better learn bacterial ecological function for plant growth. In this study, rhizosphere soil of six different chemotype Cinnamomum camphora trees were collected, including C. bodinieri var. citralifera, [C. camphora (Linn.) Presl], camphora-type, cineole-type, linalool-type and isoborneol-type. Soil properties content and bacterial communities were analyzed. Two chemotype C. camphora, including [C. camphora (Linn.) Presl] and linalool-type, shaped similar bacterial community structure, decreased Firmcutes relative abundance. richness estimators (Chao1 index and Ace index) of [C. camphora (Linn.) Presl] were decreased compared with the others. Furthermore, soil bacterial community structure was also similar among bodinieri var. citralifera, camphora-type, cineole-type and isoborneol-type. Hence, different chemotype C. camphora altered soil nutrient and shaped rhizosphere bacterial communities.

scholarly journals Distribution of antibiotic-resistant bacteria in aerobic composting of swine manure with different antibiotics

2021 ◽  
Vol 33 (1) ◽  
Author(s):  
Tingting Song ◽  
Hongna Li ◽  
Binxu Li ◽  
Jiaxun Yang ◽  
Muhammad Fahad Sardar ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Community Structure ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Bacterial Community Structure ◽  
Swine Manure ◽  
Resistant Bacteria ◽  
Absolute Abundance ◽  
Antibiotic Resistant Bacteria ◽  
Antibiotic Resistant

Abstract Background Livestock manure is an important reservoir of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs). The bacterial community structure and diversity are usually studied using high-throughput sequencing that cannot provide direct evidence for ARB changes. Thus, little is known about the distribution of ARB, especially in the presence of different antibiotics in composting process. In this study, the fate of ARB was investigated in aerobic composting of swine manure, using chlortetracycline, sulfamethoxazole, lincomycin, and ciprofloxacin as typical antibiotics. The abundance and species of ARB were analyzed systematically to evaluate their ecological risk at different stages of composting. Results The absolute abundance of total ARB decreased, while the relative abundance increased on day 2. The relative abundance of lincomycin-resistant bacteria was higher than other ARBs during the whole composting process. The absolute abundance of four ARBs was 9.42 × 106–2.51 × 102 CFU/g (lincomycin- > chlortetracycline- > sulfamethoxazole- > ciprofloxacin- > multiple antibiotic-resistant bacteria), and they were not completely inactivated at the end of composting. Antibiotics led to a partial proliferation of ARBs including Corynebacterium, Sporosarcina, Solibacillus, and Acinetobacter. Especially, Corynebacterium, a pathogenic genus, was observed in chlortetracycline and lincomycin treatments. Conclusion Among the antibiotics studied, lincomycin showed the highest ecological risk, due to it expanded the range of lincomycin-resistant bacteria at the phyla level (Firmicutes, Actinobacteria, and Proteobacteria). The principal co-ordinates analysis indicated that the bacterial community structure was primarily associated with the composting stages rather than antibiotic types. Possible potential hosts and the related to the decrease of ARGs abundance were indicated based on the network analysis. The decrease of culturable Proteobacteria and the increase of culturable Firmicutes (Solibacillus, Bacillus) partially explained the high degradation rate of various ARGs with the progress of composting in this study. These results provided important information for the control of antibiotic resistance in composting.

scholarly journals Analysis of Microbial Community Structure Around Roots of Stipa Grandis

2021 ◽  
Author(s):  
Ai-Min Zhu ◽  
Guo-Dong Han ◽  
Hai-Li Liu ◽  
Yue-Hua Wang
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Rhizosphere Soil ◽  
Root Zone ◽  
Diversity Index ◽  
Alpha Diversity ◽  
Microbial Structure ◽  
Root Epidermis ◽  
16S Rna

Abstract The root zone microbial structure is particularly complex for plants with rhizosheaths, which may play an important role in the future agricultural sustainable development. However, one of the important reasons for restricting our study of rhizosheath microbial structure is that there is no definite method for rhizosheath separation. The aim of this study was to explore the isolation methods of rhizosheath and the diversity and functional characteristics of microorganisms around the rhizosphere. In this study, we isolated the rhizosheath of Stipa grandis, a dominant species in desert steppe, and the microorganisms in the roots, root epidermis, rhizosheath, rhizosphere soil were extracted and sequenced by 16s RNA and ITS. The bacterial alpha diversity index was in the order rhizosphere soil > rhizosheath > root epidermis > endophytic, and the fungal alpha diversity index was rhizosphere soil and rhizosheath > root epidermis and endophytic. There were significant differences in bacterial community structure between the root epidermis and endophytic, rhizosheath, rhizosphere soil, and the sum of relative abundance of the dominant bacterial populations Actinobacteria and Proteobacteria was 73.9% in the root epidermis. Different from bacterial community structure, the community structure of root epidermis fungi was similar to endophytic, but significantly different from rhizosheath and rhizosphere soil. We suggest that the root epidermis can act as the interface between the host plant root and the external soil environment. This study will provide theoretical and technical guidance for the isolation of plant rhizosheath and the study of microorganisms in it.

scholarly journals Effects of ultraviolet radiation on the community structure and metabolic pathways of A2O process at Plateau environment

2021 ◽  
Author(s):  
Zong Yongchen ◽  
He Qiang ◽  
Guo Mingzhe ◽  
You Junhao ◽  
Zhang Dongyan
Keyword(s):  
Community Structure ◽  
Water Treatment ◽  
Bacterial Community ◽  
Ultraviolet Radiation ◽  
Relative Abundance ◽  
Ultraviolet Irradiation ◽  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Bacterial Community Structure ◽  
Key Species

Abstract Water treatment ecosystem provides important habitats for various bacterial communities. However, the response mechanism of this ecosystem under ultraviolet rays is not yet clear. In the study, 16S rRNA gene sequencing is used to study the bacterial community structure and metabolic pathways under 5 samples of ultraviolet irradiation times. In general, the bacterial communities of the five samples are different, which indicates that the ultraviolet radiation time has an impact on the bacterial community structure. Analysis of driving factors shows that UV, COD, pH, TN and NH3-N have an impact on the relative abundance of key species. Key species under ultraviolet irradiation are Bacteroidetes, Proteobacteria, Actinobacteria, Firmicutes, Chloroflexi, and Chlamydiae, accounting for 96.69%ཞ98.30%, and ultraviolet irradiation has a significant inhibitory effect on the relative abundance. As the dominant bacterial phyla in Plateau environment, Chlamydiae is discovered for the first time. The network co-occurrence diagrams constructed under different ultraviolet radiation show that each sample is composed of three independent network diagrams. There are 6 common dominant phyla and 33 common dominant bacterial genera in each sample, which reveals that the structure of the ecosystem is composed of more similar microorganisms, rather than random phenomena. It also reflects the competitive relationship between species and the adaptability of bacteria to the environment. Through the analysis of metabolic pathways, it is found that the dominant metabolic pathways in high altitude habitats have certain changes under ultraviolet radiation. Further analysis of carbon, nitrogen and phosphorus metabolic pathways shows that the relative abundance of related metabolic pathways has a certain change, but the difference in metabolic maps is small, that is, the effect of ultraviolet radiation is mainly reflected in the relative abundance of metabolic pathways. These findings indicate that ultraviolet radiation in Plateau environment as an important influencing factor has an impact on microbial structure and metabolic pathways. This research provides an important theoretical basis for further understanding of water treatment ecosystem in Plateau environment, and also provides a new perspective for the development of water treatment ecosystem.

scholarly journals Changes in Heterotrophic Picoplankton Community Structure after Induction of a Phytoplankton Bloom under Different Light Regimes

Diversity ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 195 ◽  
Author(s):  
Karayanni ◽  
Kormas ◽  
Moustaka-Gouni ◽  
Sommer
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Environmental Changes ◽  
Phytoplankton Bloom ◽  
Phytoplankton Growth ◽  
Light Regimes ◽  
Operational Taxonomic Units ◽  
Abundant Otus

Bacterial and archaeal diversity and succession were studied during a mesocosm experiment that investigated whether changing light regimes could affect the onset of phytoplankton blooms. For this, 454-pyrosequencing of the bacterial V1-V3 and archaeal V3-V9 16S rRNA regions was performed in samples collected from four mesocosms receiving different light irradiances at the beginning and the end of the experiment and during phytoplankton growth. In total, 46 bacterial operational taxonomic units (OTUs) with ≥1% relative abundance occurred (22–34 OTUs per mesocosm). OTUs were affiliated mainly with Rhodobacteraceae, Flavobacteriaceae and Alteromonadaceae. The four mesocosms shared 11 abundant OTUs. Dominance increased at the beginning of phytoplankton growth in all treatments and decreased thereafter. Maximum dominance was found in the mesocosms with high irradiances. Overall, specific bacterial OTUs had different responses in terms of relative abundance under in situ and high light intensities, and an early phytoplankton bloom resulted in different bacterial community structures both at high (family) and low (OTU) taxonomic levels. Thus, bacterial community structure and succession are affected by light regime, both directly and indirectly, which may have implications for an ecosystem’s response to environmental changes.

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